A hotspot mutation p.L162R in IKZF3 drives leukemogenesis via transcriptional dysregulation
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PROVIDER: PRJNA601427 | ENA |
REPOSITORIES: ENA
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Project description:IKZF3 encodes an IKAROS Family transcription factor and has been recently identified as a novel mutated gene in chronic lymphocytic leukemia (CLL), with all mutations occurring at a single hotspot (L162R), located within the DNA binding domain of the protein. Here we show that B cell-restricted conditional knock-in of this mutation skews B cells development and induces CLL-like disease in elderly mice (30% penetrance), confirming its role as a CLL driver. Furthermore, this mutation alters the DNA binding specificity and target selection of IKZ3, leading to overexpression of BCR/NF-?B signaling genes and hyperactivation of these pathways. Likewise, we find an upregulated BCR signaling signature in human CLLs with IKZF3-L162R. Our studies highlight a novel mechanism by which a CLL driver activates the critical oncogenic BCR/NF-?B signaling axis in CLL
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Project description:RNA splicing factor SF3B1 is recurrently mutated in various cancers, particularly in hematological malig-nancies. We previously reported that co-expression of Sf3b1 mutation and Atm deletion in B cells, but not either lesion alone, leads to the onset of chronic lymphocytic leukemia (CLL) with CLL cells harboring chromosome amplification. However, the exact role of Sf3b1 mutation and Atm deletion in chromosomal instability (CIN) remains unclear. Here, we demonstrate that SF3B1 mutation promotes centromeric R-loop (cen-R-loop) accumulation, leading to increased chromosome oscillation, impaired chromosome segrega-tion, altered spindle architecture and aneuploidy, which can be alleviated by removal of cen-R-loop and exaggerated by deletion of ATM. Aberrant splicing of key genes involved in R-loop processing underlies augmentation of cen-R-loop as overexpression of the normal isoform, but not the altered form, mitigates mitotic stress in SF3B1 mutant cells. Our study underscores the critical role of novel splice variants in link-ing RNA splicing dysregulation and CIN, and highlights cen-R-loop augmentation as a key mechanism for leukemogenesis.
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Project description:Additional sex comb-like 1 (ASXL1) is frequently mutated in a spectrum of myeloid malignancies and is associated with poor prognosis. Cancer genome sequencing found that AXL1 mutations frequently co-occur with splicing factors’ mutations (SRSF2, U2AF1, ZRZR2 and SF3B1) in myeloid malignancies. Several studies have reported that Patients with both ASXL1 and splicing mutations have a significantly worse prognosis than those with a single type of mutation, but the mechanisms largely remain to be elucidated. Here we constructed an ASXL1 and SRSF2 co-mutated mouse model and found that Srsf2P95H/+ mutation exacerbated Asxl1Y588XTg-induced leukemogenesis. Mechanistically, the co-existence of ASXL1 mutation and SRSF2 mutation altered the function of hematopoietic stem and progenitor cells and resulted in skewed myeloid differentiation.
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Project description:A missense change in RRAS2 (Gln72-to-Leu), analogous to the Gln61-to-Leu mutation of RAS oncoproteins, has been identified as a hotspot mutation in cancer and Noonan syndrome. However, the relevance of this mutation for in vivo tumorigenesis remains unknown. Here, we show that R-RAS2(Q72L) is required for optimal tumorigenic activity of human cancer cells.
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Project description:Recurrent somatic hotspot mutations of DICER1 appear to be clustered around each of four critical metal binding residues in the RNase IIIB domain of DICER1. This domain is responsible for cleavage of the 3’ end of the 5p-miRNA strand of a pre-mRNA hairpin. To investigate the effects of these cancer-associated “hotspot” mutations we engineered mouse Dicer1-deficient ES cells to express wild-type and an allelic series of the mutant human DICER1 variants. Global miRNA and mRNA profiles from cells carrying the metal binding site mutations were compared to each other and wild-type human DICER1. The miRNA and mRNA profiles generated through the expression of the hotspot mutations were virtually identical, and the DICER1 hotspot mutation carrying cells were distinct from both wild-type and Dicer1-deficient cells. Further, miRNA profiles showed mutant DICER1 results in a dramatic loss in processing of mature 5p-miRNA strands but were still able to create 3p-strand miRNAs. Messenger-RNA profile changes were consistent with the loss of 5p-strand miRNAs and showed enriched expression for predicted targets of the lost 5p derived miRNAs. We therefore conclude that cancer-associated somatic hotspot mutations of DICER1, affecting any one of four metal binding residues in the RNase IIIB domain, are functionally equivalent with respect to miRNA-processing and are hypomorphic alleles, yielding a global loss in processing of mature 5p-strand miRNA. We further propose that this resulting 3p-strand bias in mature miRNA expression likely underpins the oncogenic potential of these hotspot mutations. A total of 28 Affymetrix Mouse Gene ST arrays were done for mRNA expression profiling of various DICER1 mutants (n=14), wildtype controls (n=6), vector only (n=3) and parental cell lines (n=5).
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Project description:Mutation of DNA methyltransferase 3A at arginine 882 (DNMT3AR882mut) is prevalent in various hematological cancers. DNMT3AR882mut was recently shown to carry partially defective, dominant-negative or gain-of-function activities under different in vitro contexts. However, the causal roles for such a multifaceted effect of DNMT3AR882mut on leukemogenesis remain undefined. Here we report TF-1 leukemia cells as a robust system for modeling DNMT3AR882mut-dependent cell transformation phenotypes and for performing structure-function relationship studies of DNMT3AR882mut. We show that expression of DNMT3AR882mut and not its wildtype counterpart promotes TF-1 cell transformation and induces CpG hypomethylation predominantly at enhancers. Such effect by DNMT3AR882mut is dose-dependent, acts synergistically with that of IDH1 mutation, and resembles what was seen in human leukemia patients with DNMT3AR882mut. Both transformation- and hypomethylation-inducing capacities of DNMT3AR882mut rely on a motif involved in heterodimerization whereas its various chromatin-binding and enzymatic domains were dispensable. We also show bromodomain inhibition as a therapeutic means for treatment of murine leukemia carrying DNMT3AR882mut. Collectively, this study describes a useful model system for studying DNMT3AR882mut and supports a requirement for the dominant-negative effect of DNMT3AR882mut during leukemogenesis.
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Project description:The p.R482W hotspot mutation in A-type nuclear lamins causes familial partial lipodystrophy of Dunnigantype (FPLD2), a lipodystrophic syndrome complicated by early-onset atherosclerosis. Molecular mechanisms underlying endothelial cell dysfunction conferred by the lamin A mutation remain elusive. However, lamin A regulates epigenetic developmental pathways and mutations could perturb these functions. Here, we demonstrate that lamin A R482W elicits endothelial differentiation defects in a developmental model of FPLD2. Genome modeling in fibroblasts from patients with FPLD2 caused by the lamin A R482W mutation reveals repositioning of the mesodermal regulator T/Brachyury locus towards the nuclear center relative to normal fibroblasts, suggesting enhanced activation propensity of the locus in a developmental model of FPLD2. Addressing this issue, we report phenotypic and transcriptional alterations in mesodermal and endothelial differentiation of induced pluripotent stem cells we generated from a patient with R482Wassociated FPLD2. Correction of the LMNA mutation ameliorates R482W-associated phenotypes and gene expression. Transcriptomics links endothelial differentiation defects to decreased Polycomb-mediated repression of the T/Brachyury locus and over-activation of T target genes. Binding of the Polycomb repressor complex PRC2 to T/Brachyury is impaired by the mutated lamin A network, which is unable to properly associate with the locus. This leads to a deregulation of vascular gene expression over time. By connecting a lipodystrophic hotspot lamin A mutation to a disruption of early mesodermal gene expression and defective endothelial differentiation, we propose that the mutation rewires the fate of several lineages, resulting in multitissue pathogenic phenotypes.
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